toil 5.12.0__py3-none-any.whl → 6.1.0__py3-none-any.whl

toil/test/provisioners/clusterTest.py

@@ -17,8 +17,7 @@ import os
 import subprocess
 import time
 from uuid import uuid4
-
-import boto.ec2
+from typing import Optional, List
 
 from toil.lib.aws import zone_to_region
 from toil.lib.retry import retry
@@ -30,7 +29,7 @@ log = logging.getLogger(__name__)
 @needs_aws_ec2
 @needs_fetchable_appliance
 class AbstractClusterTest(ToilTest):
-    def __init__(self, methodName):
+    def __init__(self, methodName: str) -> None:
         super().__init__(methodName=methodName)
         self.keyName = os.getenv('TOIL_AWS_KEYNAME').strip() or 'id_rsa'
         self.clusterName = 'aws-provisioner-test-' + str(uuid4())
@@ -38,18 +37,20 @@ class AbstractClusterTest(ToilTest):
         self.clusterType = 'mesos'
         self.zone = get_best_aws_zone()
         assert self.zone is not None, "Could not determine AWS availability zone to test in; is TOIL_AWS_ZONE set?"
-        # We need a boto2 connection to EC2 to check on the cluster
+        # We need a boto2 connection to EC2 to check on the cluster.
+        # Since we are protected by needs_aws_ec2 we can import from boto.
+        import boto.ec2
         self.boto2_ec2 = boto.ec2.connect_to_region(zone_to_region(self.zone))
         # Where should we put our virtualenv?
         self.venvDir = '/tmp/venv'
 
-    def python(self):
+    def python(self) -> str:
         """
         Return the full path to the venv Python on the leader.
         """
         return os.path.join(self.venvDir, 'bin/python')
 
-    def pip(self):
+    def pip(self) -> str:
         """
         Return the full path to the venv pip on the leader.
         """
@@ -63,7 +64,7 @@ class AbstractClusterTest(ToilTest):
         """
         subprocess.check_call(['toil', 'destroy-cluster', '-p=aws', '-z', self.zone, self.clusterName])
 
-    def setUp(self):
+    def setUp(self) -> None:
         """
         Set up for the test.
         Must be overridden to call this method and set self.jobStore.
@@ -73,13 +74,13 @@ class AbstractClusterTest(ToilTest):
         # If this fails, no tests will run.
         self.destroyCluster()
 
-    def tearDown(self):
+    def tearDown(self) -> None:
         # Note that teardown will run even if the test crashes.
         super().tearDown()
         self.destroyCluster()
         subprocess.check_call(['toil', 'clean', self.jobStore])
 
-    def sshUtil(self, command):
+    def sshUtil(self, command: List[str]) -> None:
         """
         Run the given command on the cluster.
         Raise subprocess.CalledProcessError if it fails.
@@ -144,7 +145,18 @@ class AbstractClusterTest(ToilTest):
             raise subprocess.CalledProcessError(p.returncode, ' '.join(cmd))
 
     @retry(errors=[subprocess.CalledProcessError], intervals=[1, 1])
-    def createClusterUtil(self, args=None):
+    def rsync_util(self, from_file: str, to_file: str) -> None:
+        """
+        Transfer a file to/from the cluster.
+
+        The cluster-side path should have a ':' in front of it.
+        """
+        cmd = ['toil', 'rsync-cluster', '--insecure', '-p=aws', '-z', self.zone, self.clusterName, from_file, to_file]
+        log.info("Running %s.", str(cmd))
+        subprocess.check_call(cmd)
+
+    @retry(errors=[subprocess.CalledProcessError], intervals=[1, 1])
+    def createClusterUtil(self, args: Optional[List[str]]=None) -> None:
         args = [] if args is None else args
 
         command = ['toil', 'launch-cluster', '-p=aws', '-z', self.zone, f'--keyPairName={self.keyName}',
@@ -156,5 +168,5 @@ class AbstractClusterTest(ToilTest):
         subprocess.check_call(command)
         # If we fail, tearDown will destroy the cluster.
 
-    def launchCluster(self):
+    def launchCluster(self) -> None:
         self.createClusterUtil()

toil/test/provisioners/gceProvisionerTest.py

@@ -136,12 +136,6 @@ class AbstractGCEAutoscaleTest(ToilTest):
                         '--python', exactPython, '/home/venv']
         self.sshUtil(venv_command)
 
-        upgrade_command = ['/home/venv/bin/pip', 'install', 'setuptools==28.7.1']
-        self.sshUtil(upgrade_command)
-
-        yaml_command = ['/home/venv/bin/pip', 'install', 'pyyaml==3.12']
-        self.sshUtil(yaml_command)
-
         self._getScript()
 
         toilOptions = [self.jobStore,

toil/test/provisioners/restartScript.py

@@ -1,6 +1,7 @@
-import argparse
 import os
 
+from configargparse import ArgumentParser
+
 from toil.job import Job
 
 
@@ -9,7 +10,7 @@ def f0(job):
         raise RuntimeError('failed on purpose')
 
 if __name__ == '__main__':
-    parser = argparse.ArgumentParser()
+    parser = ArgumentParser()
     Job.Runner.addToilOptions(parser)
     options = parser.parse_args()
     rootJob = Job.wrapJobFn(f0, cores=0.5, memory='50 M', disk='50 M')

toil/test/server/serverTest.py

@@ -21,7 +21,7 @@ import uuid
 import zipfile
 from abc import abstractmethod
 from io import BytesIO
-from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple
+from typing import Optional
 from urllib.parse import urlparse
 
 try:

toil/test/sort/restart_sort.py

@@ -20,7 +20,8 @@ import codecs
 import os
 import random
 import shutil
-from argparse import ArgumentParser
+
+from configargparse import ArgumentParser
 
 from toil.common import Toil
 from toil.job import Job

toil/test/sort/sort.py

@@ -18,7 +18,8 @@ import codecs
 import os
 import random
 import shutil
-from argparse import ArgumentParser
+
+from configargparse import ArgumentParser
 
 from toil.common import Toil
 from toil.job import Job

toil/test/sort/sortTest.py

@@ -23,10 +23,10 @@ from uuid import uuid4
 from toil import resolveEntryPoint
 from toil.batchSystems.mesos.test import MesosTestSupport
 from toil.common import Toil
+from toil.exceptions import FailedJobsException
 from toil.job import Job
 from toil.jobStores.abstractJobStore import (JobStoreExistsException,
                                              NoSuchJobStoreException)
-from toil.exceptions import FailedJobsException
 from toil.lib.bioio import root_logger
 from toil.test import (ToilTest,
                        needs_aws_ec2,
@@ -34,10 +34,8 @@ from toil.test import (ToilTest,
                        needs_google_storage,
                        needs_gridengine,
                        needs_mesos,
-                       needs_parasol,
                        needs_torque,
                        slow)
-from toil.test.batchSystems.parasolTestSupport import ParasolTestSupport
 from toil.test.sort.sort import (copySubRangeOfFile,
                                  getMidPoint,
                                  main,
@@ -64,7 +62,7 @@ def runMain(options):
 
 
 @slow
-class SortTest(ToilTest, MesosTestSupport, ParasolTestSupport):
+class SortTest(ToilTest, MesosTestSupport):
     """
     Tests Toil by sorting a file in parallel on various combinations of job stores and batch
     systems.
@@ -238,15 +236,6 @@ class SortTest(ToilTest, MesosTestSupport, ParasolTestSupport):
     def testFileTorqueEngine(self):
         self._toilSort(jobStoreLocator=self._getTestJobStorePath(), batchSystem='torque')
 
-    @needs_parasol
-    @unittest.skip("skipping until parasol support is less flaky (see github issue #449")
-    def testFileParasol(self):
-        self._startParasol()
-        try:
-            self._toilSort(jobStoreLocator=self._getTestJobStorePath(), batchSystem='parasol')
-        finally:
-            self._stopParasol()
-
     testNo = 5
 
     def testSort(self):

toil/test/src/autoDeploymentTest.py

@@ -3,13 +3,13 @@ import subprocess
 import time
 from contextlib import contextmanager
 
+from toil.exceptions import FailedJobsException
 from toil.lib.iterables import concat
 from toil.test import (ApplianceTestSupport,
                        needs_local_appliance,
                        needs_mesos,
                        slow)
 from toil.version import exactPython
-from toil.exceptions import FailedJobsException
 
 logger = logging.getLogger(__name__)
 
@@ -207,28 +207,28 @@ class AutoDeploymentTest(ApplianceTestSupport):
 
     def testDeferralWithConcurrentEncapsulation(self):
         """
-        Ensure that the following DAG succeeds:
-
-                      ┌───────────┐
-                      │ Root (W1) │
-                      └───────────┘
-                            │
-                 ┌──────────┴─────────┐
-                 ▼                    ▼
-        ┌────────────────┐ ┌────────────────────┐
-        │ Deferring (W2) │ │ Encapsulating (W3) │═══════════════╗
-        └────────────────┘ └────────────────────┘               ║
-                                      │                         ║
-                                      ▼                         ▼
-                            ┌───────────────────┐      ┌────────────────┐
-                            │ Encapsulated (W3) │      │ Follow-on (W6) │
-                            └───────────────────┘      └────────────────┘
-                                      │                         │
-                              ┌───────┴────────┐                │
-                              ▼                ▼                ▼
-                      ┌──────────────┐ ┌──────────────┐ ┌──────────────┐
-                      │ Dummy 1 (W4) │ │ Dummy 2 (W5) │ │  Last (W6)   │
-                      └──────────────┘ └──────────────┘ └──────────────┘
+        Ensure that the following DAG succeeds::
+
+                          ┌───────────┐
+                          │ Root (W1) │
+                          └───────────┘
+                                │
+                     ┌──────────┴─────────┐
+                     ▼                    ▼
+            ┌────────────────┐ ┌────────────────────┐
+            │ Deferring (W2) │ │ Encapsulating (W3) │═══════════════╗
+            └────────────────┘ └────────────────────┘               ║
+                                          │                         ║
+                                          ▼                         ▼
+                                ┌───────────────────┐      ┌────────────────┐
+                                │ Encapsulated (W3) │      │ Follow-on (W6) │
+                                └───────────────────┘      └────────────────┘
+                                          │                         │
+                                  ┌───────┴────────┐                │
+                                  ▼                ▼                ▼
+                          ┌──────────────┐ ┌──────────────┐ ┌──────────────┐
+                          │ Dummy 1 (W4) │ │ Dummy 2 (W5) │ │  Last (W6)   │
+                          └──────────────┘ └──────────────┘ └──────────────┘
 
         The Wn numbers denote the worker processes that a particular job is run in. `Deferring`
         adds a deferred function and then runs for a long time. The deferred function will be
@@ -313,28 +313,28 @@ class AutoDeploymentTest(ApplianceTestSupport):
 
     def testDeferralWithFailureAndEncapsulation(self):
         """
-        Ensure that the following DAG succeeds:
-
-                      ┌───────────┐
-                      │ Root (W1) │
-                      └───────────┘
-                            │
-                 ┌──────────┴─────────┐
-                 ▼                    ▼
-        ┌────────────────┐ ┌────────────────────┐
-        │ Deferring (W2) │ │ Encapsulating (W3) │═══════════════════════╗
-        └────────────────┘ └────────────────────┘                       ║
-                                      │                                 ║
-                                      ▼                                 ▼
-                            ┌───────────────────┐              ┌────────────────┐
-                            │ Encapsulated (W3) │════════════╗ │ Follow-on (W7) │
-                            └───────────────────┘            ║ └────────────────┘
-                                      │                      ║
-                               ┌──────┴──────┐               ║
-                               ▼             ▼               ▼
-                        ┌────────────┐┌────────────┐ ┌──────────────┐
-                        │ Dummy (W4) ││ Dummy (W5) │ │ Trigger (W6) │
-                        └────────────┘└────────────┘ └──────────────┘
+        Ensure that the following DAG succeeds::
+
+                          ┌───────────┐
+                          │ Root (W1) │
+                          └───────────┘
+                                │
+                     ┌──────────┴─────────┐
+                     ▼                    ▼
+            ┌────────────────┐ ┌────────────────────┐
+            │ Deferring (W2) │ │ Encapsulating (W3) │═══════════════════════╗
+            └────────────────┘ └────────────────────┘                       ║
+                                          │                                 ║
+                                          ▼                                 ▼
+                                ┌───────────────────┐              ┌────────────────┐
+                                │ Encapsulated (W3) │════════════╗ │ Follow-on (W7) │
+                                └───────────────────┘            ║ └────────────────┘
+                                          │                      ║
+                                   ┌──────┴──────┐               ║
+                                   ▼             ▼               ▼
+                            ┌────────────┐┌────────────┐ ┌──────────────┐
+                            │ Dummy (W4) ││ Dummy (W5) │ │ Trigger (W6) │
+                            └────────────┘└────────────┘ └──────────────┘
 
         `Trigger` causes `Deferring` to crash. `Follow-on` runs next, detects `Deferring`'s
         left-overs and runs the deferred function. `Follow-on` is an instance of `Job` and the

toil/test/src/busTest.py

@@ -15,17 +15,17 @@
 import logging
 import os
 from threading import Thread, current_thread
-from typing import Optional
 
 from toil.batchSystems.abstractBatchSystem import BatchJobExitReason
-from toil.bus import JobCompletedMessage, JobIssuedMessage, MessageBus, replay_message_bus
+from toil.bus import (JobCompletedMessage,
+                      JobIssuedMessage,
+                      MessageBus,
+                      replay_message_bus)
 from toil.common import Toil
-from toil.job import Job
 from toil.exceptions import FailedJobsException
+from toil.job import Job
 from toil.test import ToilTest, get_temp_file
 
-
-
 logger = logging.getLogger(__name__)
 
 class MessageBusTest(ToilTest):

toil/test/src/checkpointTest.py

@@ -12,9 +12,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from toil.exceptions import FailedJobsException
 from toil.job import Job
 from toil.jobStores.abstractJobStore import NoSuchFileException
-from toil.exceptions import FailedJobsException
 from toil.test import ToilTest, slow
 
 
@@ -82,7 +82,7 @@ class CheckRetryCount(Job):
 
     def run(self, fileStore):
         retryCount = self.getNumRetries(fileStore)
-        fileStore.logToMaster(str(retryCount))
+        fileStore.log_to_leader(str(retryCount))
         if retryCount < self.numFailuresBeforeSuccess:
             self.addChild(AlwaysFail())
 

toil/test/src/deferredFunctionTest.py

@@ -20,8 +20,8 @@ from uuid import uuid4
 
 import psutil
 
-from toil.job import Job
 from toil.exceptions import FailedJobsException
+from toil.job import Job
 from toil.lib.threading import cpu_count
 from toil.test import ToilTest, slow
 

toil/test/src/fileStoreTest.py

@@ -29,14 +29,18 @@ from uuid import uuid4
 import pytest
 
 from toil.common import Toil
+from toil.exceptions import FailedJobsException
 from toil.fileStores import FileID
 from toil.fileStores.cachingFileStore import (CacheUnbalancedError,
                                               IllegalDeletionCacheError)
 from toil.job import Job
 from toil.jobStores.abstractJobStore import NoSuchFileException
-from toil.exceptions import FailedJobsException
 from toil.realtimeLogger import RealtimeLogger
-from toil.test import ToilTest, needs_aws_ec2, needs_google_project, needs_google_storage, slow
+from toil.test import (ToilTest,
+                       needs_aws_ec2,
+                       needs_google_project,
+                       needs_google_storage,
+                       slow)
 
 # Some tests take too long on the AWS jobstore and are unquitable for CI.  They can be
 # be run during manual tests by setting this to False.
@@ -397,6 +401,7 @@ class hidden:
             self.options.caching = True
 
         @slow
+        @pytest.mark.xfail(reason="Cannot succeed in time on small CI runners")
         def testExtremeCacheSetup(self):
             """
             Try to create the cache with bad worker active and then have 10 child jobs try to run in
@@ -472,7 +477,15 @@ class hidden:
             # the cache hence this test is redundant (caching will be free).
             if not self.options.jobStore.startswith(('aws', 'google')):
                 workDirDev = os.stat(self.options.workDir).st_dev
-                jobStoreDev = os.stat(os.path.dirname(self.options.jobStore)).st_dev
+                if self.options.jobStore.startswith("file:"):
+                    # Before #4538, options.jobStore would have the raw path while the Config object would prepend the
+                    # filesystem to the path (/path/to/file vs file:/path/to/file)
+                    # The options namespace and the Config object now have the exact same behavior
+                    # which means parse_jobstore will be called with argparse rather than with the config object
+                    # so remove the prepended file: scheme
+                    jobStoreDev = os.stat(os.path.dirname(self.options.jobStore[5:])).st_dev
+                else:
+                    jobStoreDev = os.stat(os.path.dirname(self.options.jobStore)).st_dev
                 if workDirDev == jobStoreDev:
                     self.skipTest('Job store and working directory are on the same filesystem.')
 
@@ -633,6 +646,8 @@ class hidden:
 
             Attempting to get the file from the jobstore should not fail.
             """
+            print("Testing")
+            logger.debug("Testing testing 123")
             self.options.retryCount = 0
             self.options.logLevel = 'DEBUG'
             A = Job.wrapJobFn(self._adjustCacheLimit, newTotalMB=1024, disk='1G')
@@ -655,20 +670,20 @@ class hidden:
             :param fileMB: File Size
             :return: Job store file ID for second written file
             """
-            job.fileStore.logToMaster('Double writing a file into job store')
+            job.fileStore.log_to_leader('Double writing a file into job store')
             work_dir = job.fileStore.getLocalTempDir()
             with open(os.path.join(work_dir, str(uuid4())), 'wb') as testFile:
                 testFile.write(os.urandom(fileMB * 1024 * 1024))
 
-            job.fileStore.logToMaster('Writing copy 1 and discarding ID')
+            job.fileStore.log_to_leader('Writing copy 1 and discarding ID')
             job.fileStore.writeGlobalFile(testFile.name)
-            job.fileStore.logToMaster('Writing copy 2 and saving ID')
+            job.fileStore.log_to_leader('Writing copy 2 and saving ID')
             fsID = job.fileStore.writeGlobalFile(testFile.name)
-            job.fileStore.logToMaster(f'Copy 2 ID: {fsID}')
+            job.fileStore.log_to_leader(f'Copy 2 ID: {fsID}')
 
             hidden.AbstractCachingFileStoreTest._readFromJobStoreWithoutAssertions(job, fsID)
 
-            job.fileStore.logToMaster('Writing copy 3 and returning ID')
+            job.fileStore.log_to_leader('Writing copy 3 and returning ID')
             return job.fileStore.writeGlobalFile(testFile.name)
 
         @staticmethod
@@ -680,7 +695,7 @@ class hidden:
             :param fsID: Job store file ID for the read file
             :return: None
             """
-            job.fileStore.logToMaster('Reading the written file')
+            job.fileStore.log_to_leader('Reading the written file')
             job.fileStore.readGlobalFile(fsID)
 
         # writeGlobalFile tests
@@ -794,8 +809,7 @@ class hidden:
             """
             Write a local file to the job store (hence adding a copy to cache), then have 10 jobs
             read it. Assert cached file size never goes up, assert unused job
-            required disk space is always:
-                   (a multiple of job reqs) - (number of current file readers * filesize).
+            required disk space is always ``(a multiple of job reqs) - (number of current file readers * filesize)``.
             At the end, assert the cache shows unused job-required space = 0.
             """
             self._testMultipleJobsReadGlobalFileFunction(cacheHit=True)
@@ -805,8 +819,7 @@ class hidden:
             """
             Write a non-local file to the job store(hence no cached copy), then have 10 jobs read
             it. Assert cached file size never goes up, assert unused job
-            required disk space is always:
-                   (a multiple of job reqs) - (number of current file readers * filesize).
+            required disk space is always ``(a multiple of job reqs) - (number of current file readers * filesize)``.
             At the end, assert the cache shows unused job-required space = 0.
             """
             self._testMultipleJobsReadGlobalFileFunction(cacheHit=False)
@@ -834,7 +847,10 @@ class hidden:
                 jobs[i].addChild(B)
             Job.Runner.startToil(A, self.options)
             with open(x.name) as y:
-                assert int(y.read()) > 2
+                # At least one job at a time should have been observed.
+                # We can't actually guarantee that any of our jobs will
+                # see each other currently running.
+                assert int(y.read()) > 1
 
         @staticmethod
         def _multipleFileReader(job, diskMB, fsID, maxWriteFile):
@@ -1121,7 +1137,7 @@ class hidden:
             """
 
             # Make sure we actually have the disk size we are supposed to
-            job.fileStore.logToMaster('Job is running with %d bytes of disk, %d requested' % (job.disk, jobDisk))
+            job.fileStore.log_to_leader('Job is running with %d bytes of disk, %d requested' % (job.disk, jobDisk))
             assert job.disk == jobDisk, 'Job was scheduled with %d bytes but requested %d' % (job.disk, jobDisk)
 
             cls = hidden.AbstractCachingFileStoreTest
@@ -1187,7 +1203,7 @@ class hidden:
                 try:
                     job.fileStore.deleteLocalFile(fileToDelete)
                 except IllegalDeletionCacheError:
-                    job.fileStore.logToMaster('Detected a deleted file %s.' % fileToDelete)
+                    job.fileStore.log_to_leader('Detected a deleted file %s.' % fileToDelete)
                     os.rename(tempfile, outfile)
                 else:
                     # If we are processing the write test, or if we are testing the immutably read

toil/test/src/helloWorldTest.py

@@ -24,7 +24,7 @@ class HelloWorldTest(ToilTest):
 
 class HelloWorld(Job):
     def __init__(self):
-        Job.__init__(self,  memory=100000, cores=2, disk="3G")
+        Job.__init__(self,  memory=100000, cores=1, disk="3G")
 
     def run(self, fileStore):
         fileID = self.addChildJobFn(childFn, cores=1, memory="1M", disk="3G").rv()

toil/test/src/importExportFileTest.py

@@ -18,9 +18,9 @@ import stat
 import uuid
 
 from toil.common import Toil
+from toil.exceptions import FailedJobsException
 from toil.fileStores import FileID
 from toil.job import Job
-from toil.exceptions import FailedJobsException
 from toil.test import ToilTest, slow
 
 

toil/test/src/jobDescriptionTest.py

@@ -13,7 +13,8 @@
 # limitations under the License.
 
 import os
-from argparse import ArgumentParser
+
+from configargparse import ArgumentParser
 
 from toil.common import Toil
 from toil.job import Job, JobDescription, TemporaryID

toil/test/src/jobServiceTest.py

@@ -24,9 +24,9 @@ from unittest import skipIf
 import pytest
 
 from toil.batchSystems.singleMachine import SingleMachineBatchSystem
+from toil.exceptions import FailedJobsException
 from toil.job import Job
 from toil.leader import DeadlockException
-from toil.exceptions import FailedJobsException
 from toil.lib.retry import retry_flaky_test
 from toil.test import ToilTest, get_temp_file, slow
 

toil/test/src/jobTest.py

@@ -20,8 +20,8 @@ import unittest
 import pytest
 
 from toil.common import Toil
-from toil.job import Job, JobFunctionWrappingJob, JobGraphDeadlockException
 from toil.exceptions import FailedJobsException
+from toil.job import Job, JobFunctionWrappingJob, JobGraphDeadlockException
 from toil.test import ToilTest, get_temp_file, slow
 
 logger = logging.getLogger(__name__)
@@ -37,15 +37,15 @@ class JobTest(ToilTest):
     @slow
     def testStatic(self):
         r"""
-        Create a DAG of jobs non-dynamically and run it. DAG is:
+        Create a DAG of jobs non-dynamically and run it. DAG is::
 
-        A -> F
-        \-------
-        B -> D  \
-         \       \
-          ------- C -> E
+            A -> F
+            \-------
+            B -> D  \
+             \       \
+              ------- C -> E
 
-        Follow on is marked by ->
+        Follow on is marked by ``->``
         """
         outFile = get_temp_file(rootDir=self._createTempDir())
         try:
@@ -81,15 +81,15 @@ class JobTest(ToilTest):
 
     def testStatic2(self):
         r"""
-        Create a DAG of jobs non-dynamically and run it. DAG is:
+        Create a DAG of jobs non-dynamically and run it. DAG is::
 
-        A -> F
-        \-------
-        B -> D  \
-         \       \
-          ------- C -> E
+            A -> F
+            \-------
+            B -> D  \
+             \       \
+              ------- C -> E
 
-        Follow on is marked by ->
+        Follow on is marked by ``->``
         """
         outFile = get_temp_file(rootDir=self._createTempDir())
         try:
@@ -269,7 +269,7 @@ class JobTest(ToilTest):
         identifies leaf vertices incorrectly
 
         Test verification of new checkpoint jobs being leaf verticies,
-        starting with the following baseline workflow:
+        starting with the following baseline workflow::
 
             Parent
               |
@@ -291,7 +291,7 @@ class JobTest(ToilTest):
                               omits the workflow root job
 
         Test verification of a new checkpoint job being leaf vertex,
-        starting with a baseline workflow of a single, root job:
+        starting with a baseline workflow of a single, root job::
 
             Root # Checkpoint=True
 
@@ -623,7 +623,7 @@ class JobTest(ToilTest):
         return True
 
 def simpleJobFn(job, value):
-    job.fileStore.logToMaster(value)
+    job.fileStore.log_to_leader(value)
 
 def fn1Test(string, outputFile):
     """